Detection
Molecular Beacons* allow real time PCR** detection of specific DNA sequences. Molecular Beacons can also be used to detect RNA within living cells.

Structure
Molecular Beacons are hairpin-shaped oligonucleotide probes. The loop portion of the molecule is a single-stranded DNA molecule that is complementary to a predetermined sequence in a target nucleic acid. The stem is formed by annealing two complementary arm sequences on either side of the probe sequence.

Bilabeling
Molecular Beacons are bilabeled probes, with a reporter dye on the 5 ’ -end (FAM, HEX, TET, ROX, TAMRA, Fluorescein…) and a quencher dye on the 3 ’ -end (DABCYL; BHQ). The stem keeps the reporter dye and the quencher dye in close proximity, causing the quenching of the fluorescence.

Hybridization
When the Molecular Beacon encounters a target molecule, it forms a hybrid that is longer and more stable than the hybrid formed by the arm sequences alone. Since the fluorophore is no longer in close proximity to the quencher, fluorescent emission can easily be detected.

Applications
The Molecular Beacon system is perfectly adapted for many applications namely quantitative gene analysis, automated allelic discrimination, high-throughput haplotyping, genotyping, large-scale association mapping, large-scale mutation screening and automated pathogen detection (2-7)

Sequence
Probe must contain two complementary sequences at its 5 ’ & 3 ’ extremities.

Optimal size
Up to 40 bases for the complete probe.

Reporter dyes
6-FAM, HEX, TET, Fluorescein, Cy-dyes
Special Molecular Beacons : Texas Red, Rhodamine Red, Tamra, Joe, Rox, Oregon green etc...
Dabcyl is an universal quencher
BHQ is a High-Efficiency dark quencher

Quality
Purified and verified by reverse phase HPLC and PAGE migration. Presence of labels is verified by absorbance measurements.

Quantity
1 OD, 5 OD, 10 OD, higher quantities (please contact us).

Form
Delivered in dry form

Synthesis Turn around times
8-10 working days

Design
Email us your target sequence and we will design your probes and associated primers (oligos@generalbiosystem.com)

Wavelength-shifting Molecular Beacons are brighter than conventional Molecular Beacons because of an enhancement in the intensity of the fluorescence of the emitter fluorophore. They contain a harvester fluorophore that absorbs strongly in the wavelength range of the monochromatic light source. In the presence of target DNA, probes fluoresce in the emission range of the emitter fluorophore.

Emitter fluorophore:	6-carboxyrhodamine 6G ; Tamra ; Texas Red, Cy3, Cy5, Cy5.5
Harvester fluorophore:	Commonly used: fluorescein
Quencher:	Dabcyl

* Molecular Beacon probes are sold under license from the Public Health Research Institute. They may be used under PHRI Patent Rights only for the purchaser's research and development activities.

** PCR is patented by Hoffman La Roche Ltd.

References

1 - Tyagi Sanjay and Kramer Fred Russell, (1995) - Molecular Beacons: Probes that Fluoresce
   upon Hybridization - Nature Biotechnology Volume 14 March 1996 pp 303-308
2 - Kostrikis Leondios G. , and al. (1998) - Spectral Genotyping of Human Alleles - Science
   - Vol. 279 pp 1228-1229
3 - Van Schie, and al. (2000) - Semiautomated clone verification by real-time PCR using molecular
   beacons - Biotechniques; 29(6): 1296-300, 1302-4, 1306 passim.
4 - Tyagi S, and al. (2000) - Wavelength-shifting molecular beacons - Nature Biotechnology, 18(11)
   :1191-6
5 - Kaboev OK, and al. (2000)- PCR hot start using primers with the structure of molecular beacons
   (hairpin-like structure) - Nucleic Acids Res., 28(21):E94
6 - Park S, and al.(2000) Rapid identification of Candida dubliniensis using a species-specific molecular
   beacon - J Clin Microbiol. 38(8):2829-36
7 - Chen W, and al. (2000) - Molecular Beacons : a real-time polymerase chain reaction assay for
   detecting Salmonella - Anal Biochem, 280(1):166-72